I'm a idiot for not figuring this out before, but sometimes its nice to read the directions first. :) Above is a link for instructions on modifying the game files.

One of the files you can modify is characters.

I was attempting to modify the wrong files, by designing characters, you can influence the ai races without the ability to "capture" the ai bonus's.

Via characters, I modifed the starting characters via leader and governer with +100% bonuses to ship construction, military, civilian, and colony. And 100% bonus to population. These bonus keep "growing" through out the game. So for exp, humans growth increased from approx 1% to growth 4.2%.

The ai leader will eventually get replaced, but this will give a initial boose to the ai via population. And the "bonus" for the govener will always be there. Unless the player kills the governor. :)

For the human player, dismiss the "alpha" leader, and "beta" governer. and they will be replaced by other game produced characters.

Well I have been testing giving racial bonuses to empires and it is worst than the population booster in my previous Difficulty mod because you will end up getting the bonus yourself as you include one of the races in your empire. At least with the population growth you wont get oddities like insane research bonus or whatever cheat you gave the AI. I found with my old Difficulty mod that even though you often get the bonus of population growth if you end up getting an insect race in your Empire the amount of insects you get in the Galaxy will still mean you get a challenge later on to keep on top of all the wars you will get in.

I might test this character based difficulty thing, have you tested it yourself? I wonder how much bonus this will give in the long term if it only affects 1 colony. The issues with Difficulty are late game really as it becomes a cake walk to roll over other Empires.

Ran the game in the background, the ai ran humans kept thier leader * 15 years without changing thier leader. It seem a value of 0 at the start keeps the character for the rest of the game. I don't know if 2 leaders would make the bonus's stack. But I know now that AI characters can be permently assigned to help the ai "cheat" for lack of a better word. (I also noted via the intellegence officer mission that the ai kept thier starting leaders as well. ie "alpha")

exp " ' - Appearance order: order that this character appears in the game relative to other characters. A value of zero (0) means that the character is present at the start of the game

0, alpha, 1, , Human, 7, 100, 10, 100, 11, 100, 12, 100, 5, 23, 44 "

As to bonus to race files, I noted there are very few bonus's that you can't capture, so I gave up on the idea.

My work\wife\kids home for the summer break allows me to only have a little free time during the day. So I havn't really had much of a chance to "really" test my theorys. sorry. I was hoping others could try it. thanks.

It also seems that all ai's need "limited" on the research to help them avoid filler tech's. Like dual researching missle's and torpedo's. I noted the ai ran empire kept doing research like missle fighter followed by torpedo fighter ??? Limiting the weapons research might make the ai more competitive.

Forgot to add, all skills listed below can be given +100 at the start of the game, So for exp, you could give svl fleet officers +100 to targeting, countermeasures, weaponrange, and weapon damage. If you really wanted to give the ai a boost. :)